The configuration key SysDeletedObjects40 ("Keep update objects") is meant to be turned off, but I often see it turned on in live environments.
The point of the configuration key is to mark tables and fields that are no longer used by the new standard application. The marking indicates that the table or field will be completely removed from the next version of AX.
Having the key turned on allows you to eventually upgrade your data when you upgrade from an earlier version. If you have done the upgrade or you don't need to do any upgrade, turn it off.
Turning it off removes the physical data from the datebase. For fields you will get rid of the field from select statements, which can be a great performance improvement. Take for example the CompanyInfo table where AX keeps selecting the bitmap stored in the field DEL_Logo, until you turn off this configuation key. The content of this particular field has been copied to another table during the upgrade and AX uses this other table when it actually needs the company logo image.
If 4.0 is your first AX version, i.e. you are not upgrading from an earlier version, there is absolutely no point in having the configuration key turned on.
See also "Disable Keep update objects (SysDeletedObjects40)" on MSDN.